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The branches view for one of our very active repositories shows that a branch is behind when it is not. Even deleting and re-creating the branch does not resolve the issue.
The newly created branch (with the same name) immediately shows that it is behind again the same number of commits as it incorrectly showed before we deleted it and recreated it.
The only solution I see at this point is to completely delete the repo and re-create it. Not a great situation.